Sins of the Fathers Chapter 1: Doctor Strange - S3-E1
Revealing mistake: When Mary Jane and the other servants of Baron Mordo are flying through the city, they literally disappear into thin air. Probably a problem with rendering the 2D animation within the 3D animation. (00:01:00)
Revealing mistake: When Nova blasts through the building, the wall where the hole is created has already been drawn as misshapen and discolored, likely to make it easier for the animators to animate. (00:02:53)
Rejoice! I Am Ultimo Thy Deliverer - S1-E2
Revealing mistake: When Rhodey is approaching Tony on his yacht, if you watch carefully, you can see that Rhodey appears out of thin air.